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Applying the TPS method to Modeling and Simulation of Biological Systems

Rhys Goldstein, Nada Farran, Hamel Yigang, Sanaa Lissari and Gabriel Wainer

The 2010 Summer Computer Simulation Conference (SCSC 10)
Ottawa, Canada, July 11-14, 2010


Deformable biological structures are typically modeled with the finite element method, but we have designed a much simpler impulse-based method called the "tethered particle system" (TPS). The TPS involves the use of discrete event simulation to track the positions of a large number of particles. As would be expected, two approaching particles may collide and rebound off one another. What's different is that, provided they are "tethered", two separating particles may also collide and retract inwards. This contrains the distances between pairs of particles, allowing various deformable structures to be represented.

In this article, we present the application of the TPS method to different biological system: the formation of a DNA particle, the formation of helix-shaped actin filaments, and the definition of synapsin-vesicle models including mitochondria in nerve terminals. This includes advanced visualization methods.

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